The pollution of receiving waters by overflows from combined sewers is a national problem of serious concern. A recent viable solution strategy for the problem involves the development of automatic control systems as an alternative to more expensive sewer separation or large-scale treatment projects. Development of the control logic is difficult, due mainly to the size and complexity of the problem. A hierarchical control strategy is developed and applied to the proposed San Francisco Master Plan for Wastewater Management. The large-scale problem is decomposed into several first-level subbasin problems, with a second level master problem tying them together. An aggregation approach is also presented as another way of developing a hierarchical control structure. The subbasin problems can be solved either on-line of off-line, depending on the complexity of the sewer transport models utilized.